Home LiteratureArticle Details

PMID: 23778453 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing.

RNA biology ·Vol. 10 ·No. 7 ·2013-07-00 ·Pages 1087-92

Wu J, Liu Q, Wang X, Zheng J, Wang T, You M, Sheng Sun Z, Shi Q

Abstract

Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in a cost-effective way. In this study, we developed mirTools 2.0, an updated version of mirTools 1.0, which includes the following new features. (1) From miRNA discovery in mirTools 1.0, mirTools 2.0 allows users to detect and profile various types of ncRNAs, such as miRNA, tRNA, snRNA, snoRNA, rRNA, and piRNA. (2) From miRNA profiling in mirTools 1.0, mirTools 2.0 allows users to identify miRNA-targeted genes and performs detailed functional annotation of miRNA targets, including Gene Ontology, KEGG pathway and protein-protein interaction. (3) From comparison of two samples for differentially expressed miRNAs in mirTools 1.0, mirTools 2.0 allows users to detect differentially expressed ncRNAs between two experimental groups or among multiple samples. (4) Other significant improvements include strategies used to detect novel miRNAs and piRNAs, more taxonomy categories to discover more known miRNAs and a stand-alone version of mirTools 2.0. In conclusion, we believe that mirTools 2.0 (122.228.158.106/mr2_dev and centre.bioinformatics.zj.cn/mr2_dev) will provide researchers with more detailed insight into small RNA transcriptomes.

Keywords

miRNA miRNA targets mirTools ncRNA next-generation sequencing web server

MeSH Terms

Computational Biology/methods Databases, Nucleic Acid High-Throughput Nucleotide Sequencing Internet MicroRNAs/genetics,metabolism Molecular Sequence Annotation RNA, Untranslated Transcriptome

Chemicals

MicroRNAs RNA, Untranslated

Authors & Affiliations

8 authors, click to expand affiliations / ORCID

Wu Jinyu

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences; University of Science and Technology of China; Hefei, China; Institute of Genomic Medicine; Wenzhou Medical College; Wenzhou, China.

Liu Qi

Wang Xin

Zheng Jiayong

Wang Tao

You Mingcong

Sheng Sun Zhong

Shi Qinghua

References (36)

36 references, click to expand

Non-coding RNAS: A new member of the family.
Nat Rev Mol Cell Biol. 2012 Nov;13(11):686 PMID: 23011341
YM500: a small RNA sequencing (smRNA-seq) database for microRNA research.
Nucleic Acids Res. 2013 Jan;41(Database issue):D285-94 PMID: 23203880
Small RNA transcriptome investigation based on next-generation sequencing technology.
J Genet Genomics. 2011 Nov 20;38(11):505-13 PMID: 22133681
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W68-76 PMID: 19433510
Mireval: a web tool for simple microRNA prediction in genome sequences.
Bioinformatics. 2008 Jun 1;24(11):1394-6 PMID: 18453555
miRNAkey: a software for microRNA deep sequencing analysis.
Bioinformatics. 2010 Oct 15;26(20):2615-6 PMID: 20801911
Roles for microRNAs in conferring robustness to biological processes.
Cell. 2012 Apr 27;149(3):515-24 PMID: 22541426
The significance of digital gene expression profiles.
Genome Res. 1997 Oct;7(10):986-95 PMID: 9331369
miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data.
Genome Biol. 2010;11(4):R39 PMID: 20370911
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans.
BMC Bioinformatics. 2007 Sep 17;8:341 PMID: 17868480
Spliceosomal snRNA modifications and their function.
RNA Biol. 2010 Mar-Apr;7(2):192-204 PMID: 20215871
Small RNAs derived from snoRNAs.
RNA. 2009 Jul;15(7):1233-40 PMID: 19474147
Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms.
Annu Rev Genet. 2011;45:447-69 PMID: 21942366
Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis.
Nucleic Acids Res. 2012 May;40(9):4013-24 PMID: 22266655
DSAP: deep-sequencing small RNA analysis pipeline.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W385-91 PMID: 20478825
Cytoscape Web: an interactive web-based network browser.
Bioinformatics. 2010 Sep 15;26(18):2347-8 PMID: 20656902
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
Nucleic Acids Res. 2012 Jan;40(1):37-52 PMID: 21911355
Discovering microRNAs from deep sequencing data using miRDeep.
Nat Biotechnol. 2008 Apr;26(4):407-15 PMID: 18392026
SOAP2: an improved ultrafast tool for short read alignment.
Bioinformatics. 2009 Aug 1;25(15):1966-7 PMID: 19497933
CPSS: a computational platform for the analysis of small RNA deep sequencing data.
Bioinformatics. 2012 Jul 15;28(14):1925-7 PMID: 22576177
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
KEGG for representation and analysis of molecular networks involving diseases and drugs.
Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60 PMID: 19880382
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W112-7 PMID: 21622957
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.
Bioinformatics. 2010 Sep 15;26(18):2226-34 PMID: 20591903
A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity.
Cell. 2012 Apr 27;149(3):693-707 PMID: 22541438
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Bioinformatics. 2011 Nov 15;27(22):3202-3 PMID: 21976421
miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression.
BMC Bioinformatics. 2009 Oct 12;10:328 PMID: 19821977
smyRNA: a novel Ab initio ncRNA gene finder.
PLoS One. 2009;4(5):e5433 PMID: 19415115
mirTools: microRNA profiling and discovery based on high-throughput sequencing.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W392-7 PMID: 20478827
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants.
Bioinformatics. 2011 Sep 15;27(18):2614-5 PMID: 21775303
ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data.
Bioinformatics. 2012 Dec 1;28(23):3147-9 PMID: 23044543
A k-mer scheme to predict piRNAs and characterize locust piRNAs.
Bioinformatics. 2011 Mar 15;27(6):771-6 PMID: 21224287
Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis.
Nucleic Acids Res. 2012 May;40(10):4298-305 PMID: 22287634
Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data.
Nucleic Acids Res. 2012 Sep;40(16):7633-43 PMID: 22705792
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6 PMID: 18940858
shortran: a pipeline for small RNA-seq data analysis.
Bioinformatics. 2012 Oct 15;28(20):2698-700 PMID: 22914220

Article Info

Journal

RNA biology

Abbr.

RNA Biol

ISSN

1555-8584

DOI

10.4161/rna.25193

Published

2013-07-00

Epub

2013-00-29

Pages

1087-92

Language

English

Region

United States

NLM ID

101235328

PMCID

PMC3849156

Subset

External Links

PubMed source DOI: 10.4161/rna.25193 PMC Full Text View journal details

Analysis Services

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing.

Contact

WeChat Official Account